The radionuclide content of the isolated acyl-CoA molecular species does not yield a reliable measurement of these materials. One method involves reductive de-acylation of the acyl-CoA species to generate the corresponding fatty alcohols, which are then converted to pentafluorobenzoyl derivatives and analyzed by GC-NICI-MS. This method is laborious, and the analyte is lost during reduction and derivatization. Our preliminary results from the ZAB-SE using Fast Atom Bombardment-mass spectrometry demonstrate that a S/N >10 can be obtained from 10 pmol injection each of myristoyl-, heptadecanoyol-and dodecanoyol-CoA. The salts (mainly Na+ and K+) were removed by cation ion exchange resin or DEAE-cellulose. The same FAB-MS responses obtained from equal amount mix of C12-, C14-, and C16- CoA suggest that quantitation of these compounds using C13-, C15-, and C17-CoA as internal standard can be performed.